Mercurial > repos > eric-rasche > circos
annotate macros_conffiles.xml @ 7:b72f2db6d417 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 86fb40a41d9e6012ea0b02d1cd77675f4bd971fb
author | eric-rasche |
---|---|
date | Sat, 10 Jun 2017 14:16:41 -0400 |
parents | 169adf243c0a |
children | eb3af6e9f633 |
rev | line source |
---|---|
0
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
2 <macros> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
3 <xml name="configfile_circos_conf"> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
4 <configfile name="circos_conf"><![CDATA[ |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
5 <<include colors_fonts_patterns.conf>> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
6 <<include housekeeping.conf>> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
7 karyotype = karyotype.txt |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
8 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
9 <image> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
10 <<include etc/image.conf>> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
11 </image> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
12 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
13 <<include ticks.conf>> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
14 <<include ideogram.conf>> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
15 <plots> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
16 <<include 2d.conf>> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
17 <<include plot_highlight.conf>> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
18 </plots> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
19 <links> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
20 <<include links.conf>> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
21 </links> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
22 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
23 <<include highlight.conf>> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
24 ]]></configfile> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
25 </xml> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
26 <xml name="configfile_ticks_conf"> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
27 <configfile name="ticks_conf"><![CDATA[ |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
28 show_ticks = ${ticks.show_ticks} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
29 show_tick_labels = yes |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
30 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
31 #def circosColor($value) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
32 #set $value = str($value) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
33 #set $r = int($value[1:3], 16) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
34 #set $g = int($value[3:5], 16) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
35 #set $b = int($value[5:], 16) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
36 $r, $g, $b |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
37 #end def |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
38 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
39 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
40 <ticks> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
41 radius = ${ticks.radius}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
42 color = $circosColor($ticks.color) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
43 thickness = 2p |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
44 multiplier = ${ticks.multiplier} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
45 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
46 #for $tick_group in $ticks.tick_group: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
47 <tick> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
48 spacing = ${tick_group.spacing} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
49 size = ${tick_group.size}p |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
50 show_label = ${tick_group.show_tick_labels} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
51 label_size = ${tick_group.label_size}p |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
52 label_offset = ${tick_group.label_offset}p |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
53 format = ${tick_group.format} kb |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
54 ## TODO: figure out automated tick labels |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
55 ##if ${ticks.multiplier} * ${tick_group.spacing} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
56 </tick> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
57 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
58 </ticks> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
59 ]]> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
60 </configfile> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
61 </xml> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
62 <xml name="configfile_ideogram_conf"> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
63 <configfile name="ideogram_conf"><![CDATA[ |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
64 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
65 <ideogram> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
66 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
67 <spacing> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
68 ## spacing between ideograms |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
69 default = ${ideogram.spacing}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
70 </spacing> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
71 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
72 # ideogram position, thickness and fill |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
73 radius = ${ideogram.radius}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
74 thickness = ${ideogram.thickness}p |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
75 fill = yes |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
76 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
77 show_label = ${ideogram.ideogram_labels.show_label} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
78 label_radius = dims(ideogram,radius) + 0.075r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
79 label_size = 24 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
80 label_parallel = ${ideogram.ideogram_labels.parallel} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
81 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
82 show_bands = yes |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
83 fill_bands = yes |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
84 band_transparency = 4 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
85 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
86 </ideogram> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
87 ]]></configfile> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
88 </xml> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
89 <xml name="configfile_data_conf"> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
90 <configfile name="data_conf"><![CDATA[ |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
91 #for $hi, $data in enumerate($sec_tdd.data): |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
92 <plot> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
93 #set plot_type = str($data.plot_format.plot_format_select) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
94 #def circosColor($value) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
95 #set $value = str($value) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
96 #set $r = int($value[1:3], 16) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
97 #set $g = int($value[3:5], 16) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
98 #set $b = int($value[5:], 16) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
99 $r, $g, $b |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
100 #end def |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
101 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
102 type = ${plot_type} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
103 file = data/data-${hi}.txt |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
104 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
105 r1 = ${data.r1}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
106 r0 = ${data.r0}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
107 orientation = ${data.orientation} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
108 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
109 #if str($plot_type) == 'histogram': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
110 extend_bin = ${data.plot_format.format_specific.extend_bins} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
111 fill_color = ${data.plot_format.format_specific.fill_color} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
112 #else if str($plot_type) == 'heatmap': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
113 fill_color = $circosColor($data.plot_format.format_specific.fill_color) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
114 scale_log_base = ${data.plot_format.format_specific.scale_log_base} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
115 #else if str($plot_type) == 'line': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
116 color = $circosColor($data.plot_format.format_specific.color) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
117 thickness = ${data.plot_format.format_specific.thickness} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
118 #else if str($plot_type) == 'scatter': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
119 glyph = ${data.plot_format.format_specific.glyph} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
120 glyph_size = ${data.plot_format.format_specific.glyph_size} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
121 color = $circosColor($data.plot_format.format_specific.color) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
122 stroke_color = $circosColor($data.plot_format.format_specific.stroke_color) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
123 stroke_thickness = ${data.plot_format.format_specific.stroke_thickness} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
124 #else if str($plot_type) == 'tile': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
125 color = ${data.plot_format.format_specific.color} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
126 stroke_color = $circosColor($data.plot_format.format_specific.color) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
127 stroke_thickness = ${data.plot_format.format_specific.stroke_thickness} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
128 layers = ${data.plot_format.format_specific.layers} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
129 thickness = ${data.plot_format.format_specific.thickness} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
130 padding = ${data.plot_format.format_specific.padding} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
131 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
132 layers_overflow = ${data.plot_format.format_specific.overflow.overflow_behavior} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
133 #if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide": |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
134 layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
135 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
136 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
137 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
138 <rules> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
139 #for $rule in $data.sec_rule.rules: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
140 <rule> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
141 #for $condition in $rule.conditions |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
142 #if str($condition.application.application_select) == "1": |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
143 condition = 1 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
144 #elif str($condition.application.application_select) == "on": |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
145 #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ]) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
146 condition = $on_str |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
147 #elif str($condition.application.application_select) == "pos": |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
148 #if $condition.application.pos_gt != 0: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
149 condition = var(start) > $condition.application.pos_gt |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
150 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
151 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
152 #if $condition.application.pos_lt != 0: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
153 condition = var(start) < $condition.application.pos_lt |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
154 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
155 #elif str($condition.application.application_select) == "value": |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
156 #if $condition.application.pos_gt != 0: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
157 condition = var(value) > $condition.application.pos_gt |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
158 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
159 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
160 #if $condition.application.pos_lt != 0: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
161 condition = var(value) < $condition.application.pos_lt |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
162 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
163 #elif str($condition.application.application_select) == "var": |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
164 condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}" |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
165 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
166 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
167 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
168 #for $action in $rule.actions: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
169 #set x_fill_color = $action.action.action_value |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
170 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) + 1 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
171 #set x_fill_color_qw = ' '.join(["%s-%s" % ($action.action.action_value, $i) for i in range(1, $x_fill_color_count)]) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
172 |
5
b25b3518c2ce
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2
eric-rasche
parents:
0
diff
changeset
|
173 #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" : |
0
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
174 fill_color = eval(qw(${x_fill_color_qw})[remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, 0, ${x_fill_color_count - 1})]) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
175 #else |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
176 $action.action.action_select = ${action.action.action_value} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
177 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
178 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
179 $rule.continue_flow |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
180 </rule> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
181 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
182 </rules> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
183 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
184 <axes> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
185 #for $axis in $data.sec_axes.axes: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
186 <axis> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
187 color = $circosColor($axis.color) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
188 thickness = ${axis.thickness} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
189 spacing = ${axis.spacing}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
190 y0 = ${axis.y0}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
191 y1 = ${axis.y1}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
192 </axis> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
193 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
194 </axes> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
195 <backgrounds> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
196 #for $bkg in $data.sec_bkgs.backgrounds: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
197 <background> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
198 color = $circosColor($bkg.color) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
199 y0 = ${bkg.y0}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
200 y1 = ${bkg.y1}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
201 </background> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
202 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
203 </backgrounds> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
204 </plot> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
205 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
206 ]]></configfile> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
207 </xml> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
208 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
209 <xml name="configfile_links_conf"> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
210 <configfile name="links_conf"><![CDATA[ |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
211 #for $hi, $data in enumerate($sec_links.data): |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
212 <link> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
213 #def circosColor($value) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
214 #set $value = str($value) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
215 #set $r = int($value[1:3], 16) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
216 #set $g = int($value[3:5], 16) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
217 #set $b = int($value[5:], 16) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
218 $r, $g, $b |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
219 #end def |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
220 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
221 file = data/links-${hi}.txt |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
222 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
223 radius = ${data.radius}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
224 ribbon = ${data.linktype.ribbon} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
225 #if $data.linktype.ribbon == 'yes' |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
226 ${data.linktype.twist} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
227 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
228 color = $circosColor($data.color) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
229 bezier_radius = ${data.bezier_radius}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
230 thickness = ${data.thickness} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
231 crest = ${data.advanced.crest} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
232 bezier_radius_purity = ${data.advanced.bezier_radius_purity} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
233 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
234 #if $data.advanced.perturbation.perturb == 'yes' |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
235 perturb = yes |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
236 perturb_crest = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
237 perturb_bezier_radius = ${data.advanced.perturbation.perturb_bezier_radius_min},${data.advanced.perturbation.perturb_bezier_radius_max} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
238 perturb_bezier_radius_purity = ${data.advanced.perturbation.perturb_bezier_radius_purity_min},${data.advanced.perturbation.perturb_bezier_radius_purity_max} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
239 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
240 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
241 #if $data.advanced.zdepth |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
242 z = ${data.advanced.zdepth} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
243 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
244 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
245 <rules> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
246 #for $rule in $data.sec_link_rule.rules: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
247 <rule> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
248 #for $condition in $rule.conditions |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
249 #set cond = $condition.application.application_select |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
250 #if $cond == 'interchr' or $cond == 'intrachr' or $cond == 'inv' or $cond == 'rev' |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
251 condition = var($cond) |
6
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
252 #elif $cond == 'always' |
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
253 condition = 1 |
0
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
254 #else |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
255 #set op = $condition.application.comparison.compare |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
256 #set val = $condition.application.comparison.compval |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
257 #if $cond == 'chr' |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
258 #if $op == 'between' or $op == 'fromto' |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
259 #set val2 = $condition.application.comparison.compval2 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
260 #set c=''.join([str($op),"(",str($val),",",str($val2),")"]) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
261 #else |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
262 #set c=''.join([str($op),"(",str($val),")"]) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
263 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
264 condition = $c |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
265 #else |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
266 #if $cond == 'dist' and $op == 'lt' |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
267 condition = abs(var(pos1) - var(pos2)) < $val |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
268 #elif $cond == 'dist' and $op == 'gt' |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
269 condition = abs(var(pos1) - var(pos2)) > $val |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
270 #elif $op == 'lt' |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
271 condition = var($cond) < $val |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
272 #elif $op == 'gt' |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
273 condition = var($cond) > $val |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
274 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
275 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
276 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
277 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
278 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
279 #for $action in $rule.actions: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
280 #set actiontype = $action.action.action_select |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
281 #if $actiontype == 'color': |
6
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
282 #if $action.action.dynamic.dynamic_select == "static": |
7
b72f2db6d417
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 86fb40a41d9e6012ea0b02d1cd77675f4bd971fb
eric-rasche
parents:
6
diff
changeset
|
283 #set actionval = $circosColor($action.action.dynamic.action_value) |
6
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
284 $actiontype = $actionval |
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
285 #else |
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
286 #set x_fill_color = $action.action.dynamic.action_value |
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
287 #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) + 1 |
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
288 #set x_fill_color_qw = ' '.join(["%s-%s" % ($action.action.dynamic.action_value, $i) for i in range(1, $x_fill_color_count)]) |
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
289 $actiontype = eval(qw(${x_fill_color_qw})[remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, 0, ${x_fill_color_count - 1})]) |
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
290 #end if |
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
291 #else |
7
b72f2db6d417
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 86fb40a41d9e6012ea0b02d1cd77675f4bd971fb
eric-rasche
parents:
6
diff
changeset
|
292 #set actionval = $action.action.action_value |
6
169adf243c0a
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec
eric-rasche
parents:
5
diff
changeset
|
293 $actiontype = $actionval |
0
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
294 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
295 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
296 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
297 $rule.continue_flow |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
298 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
299 </rule> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
300 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
301 </rules> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
302 </link> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
303 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
304 ]]></configfile> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
305 </xml> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
306 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
307 <xml name="configfile_plot_highlight_conf"> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
308 <configfile name="plot_highlight_conf"><![CDATA[ |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
309 ###for $hi, $highlight in enumerate($sec_heat.highlights): |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
310 ## #if $highlight.type_select == "plot_highlights": |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
311 ##<plot> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
312 ## type = highlight |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
313 ## file = data/highlight-${hi}.txt |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
314 ## r1 = ${highlight.r1}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
315 ## r0 = ${highlight.r0}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
316 ## color = ${highlight.fill_color} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
317 ##</plot> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
318 ## #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
319 ###end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
320 ]]></configfile> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
321 </xml> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
322 <xml name="configfile_highlight_conf"> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
323 <configfile name="highlight_conf"><![CDATA[ |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
324 ##<highlights> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
325 ###for $hi, $highlight in enumerate($sec_heat.highlights): |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
326 ## #if $highlight.type_select == "normal": |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
327 ## <highlight> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
328 ## file = data/highlight-${hi}.txt |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
329 ## r1 = ${highlight.r1}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
330 ## r0 = ${highlight.r0}r |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
331 ## color = ${highlight.fill_color} |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
332 ## </highlight> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
333 ## #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
334 ###end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
335 ##</highlights> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
336 ]]></configfile> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
337 </xml> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
338 <xml name="test_case"> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
339 <configfile name="test_case_conf"><![CDATA[ |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
340 <!-- |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
341 mkdir -p test-data/my-test-case/; |
5
b25b3518c2ce
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2
eric-rasche
parents:
0
diff
changeset
|
342 #if $reference_genome.reference_genome_source == 'history': |
b25b3518c2ce
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2
eric-rasche
parents:
0
diff
changeset
|
343 cp ${genome_fasta} test-data/my-test-case/input.fa; |
b25b3518c2ce
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2
eric-rasche
parents:
0
diff
changeset
|
344 #end if |
0
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
345 #if $ideogram.bands: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
346 cp ${ideogram.bands} test-data/my-test-case/bands.${ideogram.bands.ext}; |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
347 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
348 #for $idx, $data in enumerate($sec_tdd.data): |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
349 #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'): |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
350 #for $jdx, $file in enumerate($data.plot_format.data_source): |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
351 cp ${file} test-data/my-test-case/${idx}-${jdx}.${file.ext}; |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
352 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
353 #else |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
354 cp ${data.plot_format.data_source} test-data/my-test-case/${idx}.${data.plot_format.data_source.ext}; |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
355 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
356 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
357 cp "$output_png" test-data/my-test-case/output.png; |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
358 cp "$output_svg" test-data/my-test-case/output.svg; |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
359 --> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
360 <test> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
361 <param name="reference_genome|reference_genome_source" value="${reference_genome.reference_genome_source}"/> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
362 <param name="reference_genome|genome_fasta" value="my-test-case/input.fa" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
363 <!-- ideograms --> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
364 <param name="ideogram|spacing" value="${ideogram.spacing}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
365 <param name="ideogram|radius" value="${ideogram.radius}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
366 <param name="ideogram|thickness" value="${ideogram.thickness}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
367 <param name="ideogram|ideogram_labels|show_label" value="${ideogram.ideogram_labels.show_label}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
368 <param name="ideogram|ideogram_labels|parallel" value="${ideogram.ideogram_labels.parallel}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
369 #if $ideogram.bands: |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
370 <param name="ideogram|bands" value="my-test-case/bands.${ideogram.bands.ext}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
371 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
372 <!-- Ticks --> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
373 <param name="ticks|show_ticks" value="${ticks.show_ticks}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
374 <param name="ticks|radius" value="${ticks.radius}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
375 <param name="ticks|color" value="${ticks.color}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
376 <param name="ticks|multiplier" value="${ticks.multiplier}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
377 #for $idx, $tick_group in enumerate($ticks.tick_group): |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
378 <param name="ticks|tick_group_${idx}|tickspacing" value="${tick_group.spacing}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
379 <param name="ticks|tick_group_${idx}|size" value="${tick_group.size}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
380 <param name="ticks|tick_group_${idx}|show_tick_labels" value="${tick_group.show_tick_labels}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
381 <param name="ticks|tick_group_${idx}|label_size" value="${tick_group.label_size}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
382 <param name="ticks|tick_group_${idx}|label_offset" value="${tick_group.label_offset}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
383 <param name="ticks|tick_group_${idx}|label_format" value="${tick_group.format}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
384 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
385 <!-- Data --> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
386 #for $idx, $data_group in enumerate($sec_tdd.data): |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
387 <param name="sec_tdd|data_${idx}|r0" value="${data_group.r0}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
388 <param name="sec_tdd|data_${idx}|r1" value="${data_group.r1}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
389 <param name="sec_tdd|data_${idx}|orientation" value="${data_group.orientation}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
390 <param name="sec_tdd|data_${idx}|plot_format|plot_format_select" value="${data_group.plot_format.plot_format_select}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
391 <!-- Note, please double check your files --> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
392 #if str($data_group.plot_format.plot_format_select) == 'histogram': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
393 #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)]) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
394 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
395 <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
396 <param name="sec_tdd|data_${idx}|plot_format|format_specific|extend_bins" value="${data_group.plot_format.format_specific.extend_bins}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
397 #else if str($data_group.plot_format.plot_format_select) == 'heatmap': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
398 #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)]) |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
399 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
400 <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
401 <param name="sec_tdd|data_${idx}|plot_format|format_specific|scale_log_base" value="${data_group.plot_format.format_specific.scale_log_base}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
402 #else if str($data_group.plot_format.plot_format_select) == 'line': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
403 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
404 <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
405 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke" value="${data_group.plot_format.format_specific.stroke}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
406 #else if str($data_group.plot_format.plot_format_select) == 'scatter': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
407 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
408 <param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph" value="${data_group.plot_format.format_specific.glyph}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
409 <param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph_size" value="${data_group.plot_format.format_specific.glyph_size}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
410 <param name="sec_tdd|data_${idx}|plot_format|format_specific|data_min" value="${data_group.plot_format.format_specific.data_min}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
411 <param name="sec_tdd|data_${idx}|plot_format|format_specific|data_max" value="${data_group.plot_format.format_specific.data_max}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
412 <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
413 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_color" value="${data_group.plot_format.format_specific.stroke_color}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
414 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
415 #else if str($data_group.plot_format.plot_format_select) == 'tile': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
416 <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
417 <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
418 <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
419 <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
420 <param name="sec_tdd|data_${idx}|plot_format|format_specific|layers" value="${data_group.plot_format.format_specific.layers}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
421 <param name="sec_tdd|data_${idx}|plot_format|format_specific|thickness" value="${data_group.plot_format.format_specific.thickness}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
422 <param name="sec_tdd|data_${idx}|plot_format|format_specific|padding" value="${data_group.plot_format.format_specific.padding}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
423 <param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|overflow_behavior" value="${data_group.plot_format.format_specific.overflow.overflow_behavior}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
424 #if str($data_group.plot_format.format_specific.overflow.overflow_behavior) != 'hide': |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
425 <param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|layer_overflow_color" value="${data_group.plot_format.format_specific.overflow.layer_overflow_color}" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
426 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
427 #end if |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
428 ## Next line intentionally blank |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
429 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
430 #end for |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
431 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
432 |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
433 <!-- Outputs --> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
434 <output name="output_png" file="my-test-case/output.png" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
435 <output name="output_svg" file="my-test-case/output.svg" /> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
436 </test> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
437 ]]></configfile> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
438 </xml> |
e8475d0195fe
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd
eric-rasche
parents:
diff
changeset
|
439 </macros> |